Evolv&Morph

(Last update : August 07, 2023)

• Project researchers in Toyota Central R&D Labs., Inc. : Joohwi Lee, Junpei Oba, Nobuko Ohba, and Seiji Kajita.

Evolv&Morph is a useful inverse design scheme.

This is applied to create a crystal structure reproducing a given XRD pattern.

This program involves:

• Evolutionary algorithm : modified parts of USPEX for XRD application
  

  See original code of USPEX 9.4.4 developed by Prof. Oganov et al., https://uspex-team.org)

• Crystal morphing (Oba and Kajita, Phys. Rev. Mater. 6, 023801 (2022)) and bayesian optimization for XRD application

• Other XRD-related tools

Installation

It is recommended to use ubuntu. (Mac might be fine.)

The result in the paper is obtained using ubuntu18.04, python3.7.

The last test was done (June 19, 2023) using ubuntu18.04 and python3.9 created in docker.

1. Download Evolv&Morph code from github.

2. Update apt-get and install common/required packages. (sudo apt-get could be needed sometimes.)
   Note that some of them are essential, but some of them are not so.

apt-get update --yes

apt-get install --yes --no-install-recommends wget ca-certificates sudo locales fonts-liberation

apt-get install --yes --no-install-recommends file git less nano patch tzdata unzip vim

apt-get install --yes --no-install-recommends gnuplot ghostscript epstool epstool fig2dev pstoedit

apt-get install --yes --no-install-recommends octave

apt-get install --yes --no-install-recommends openssh-client

apt-get install --yes --no-install-recommends firefox

3. install required programs via mambaforge or pip (other conda such as miniconda might be fine.)

wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh

bash ./Mambaforge-Linux-x86_64.sh

mamba install --quiet --yes ipywidgets widgetsnbextension

mamba install --quiet --yes numpy=1.23.1 scipy pandas matplotlib ipympl zstandard zstd openssl

mamba install --quiet --yes ase networkx pymatgen==2020.12.31 sympy

mamba install --quiet --yes blas lapack libblas

mamba install --quiet --yes gpy==1.10.0 gpyopt==1.2.6 paramz==0.9.5

mamba install --quiet --yes gcc gfortran make nglview

mamba install --quiet --yes notebook nb_conda_kernels

mamba clean --all -f -y

pip install rise

Note that rise is installed via pip at python3.9. Mamba make error.

4. Install GSAS-II for simulation of XRD from cif file.

For the detail, see installation pages of GSAS-II.

https://subversion.xray.aps.anl.gov/trac/pyGSAS/wiki/LinuxSingleStepInstaller

https://gsas-ii.readthedocs.io/en/latest/packages.html

mamba install --quiet --yes wxpython

mamba install --quiet --yes pyopengl pillow h5py imageio subversion

svn co https://subversion.xray.aps.anl.gov/pyGSAS/trunk ~/GSASII

python ~/GSASII/GSASIIscriptable.py

Note that wxpython is successfully installed at python3.9, but failed at python3.7.

After installation, the installed GSASII folder should be added at ~/.bashrc.

export PYTHONPATH=/home/[user name]/GSASII:$PYTHONPATH

Installation of evolutionary algorithm (USPEX)

USPEX 9.4.4 with matlab/octave was modified for XRD application.

In addition, some grammars of old octave and python2.7 was modified to work well in the newer version.

See https://uspex-team.org/en/uspex/downloads for original code.

1. According to the original code installation, USPEX 9.4.4 should be installed.

2. Overwrite all the files and folders of modified part of USPEX in this code (./uspex_modified_for_xrd) into the installed USPEX folder.
   

cp -a -r ./uspex_modified_for_xrd/* [the folder USPEX is installed]

Here, -a option preserve the permission. This keeps -x permision for USPEX and other python files in the subfolders.

3. At ~/.bashrc, the followings should be added.

export PATH=[the folder USPEX is installed]:$PATH

export USPEXPATH=[the folder USPEX is installed]/src

Additional installation of crystal morphing

Crystal morphing and its application can be directly performed at the folder.

However, the following procedure is essential prior to using it.

1. Compile SOAP.

cd ./crystal_morphing_with_bayesian_for_xrd/crystal_morphing_main/soap/_soap

bash f2pyCompile.sh 1> stdout.log 2> >(tee stderr.log >&2)

cd ../../../..

2. Patch matplot and GpyOpt installed by mambaforge.

   Do patch for avoiding errors for matplotlib and gpyopt related to version issue.
   

   It is needed to know where matplotlib and gpyopt were installed by mambaforge (or conda).
   

find [mamba-basic-folder]/envs/[mamba-env-name] -name batch_local_penalization.py -exec cp ./patches/batch_local_penalization.py {} \;

patch -b `find [mamba-basic-folder]/envs/[mamba-env-name] -name plot_definitions.py |grep matplot` ./patches/plot_definitions.py.patch

For detail, see SheffieldML/GPy#960

If the following error occurs, see grammar related to -exec at https://stackoverflow.com/questions/2961673/find-missing-argument-to-exec

find: missing argument to `-exec 

3. If the following error occurs from Bayesian optimization, numpy>1.24 should be downgrade into numpy1.23.1.

AttributeError: module 'numpy' has no attribute 'bool'. <br>
`np.bool` was a deprecated alias for the builtin `bool`. ...

mamba uninstall numpy ; mamba install numpy=1.23.1

Run evolutionary algorithm (./uspex_example_for_xrd)

How to run is written in jupyter notebook, evolutionary_algorithm_vs_target_xrd_csv_without_DFT.ipynb

If DFT calculation (VASP) is used as a supporting structural optimizer, additional setting is necessary.

Detailed information is written in jupyter notebook, evolutionary_algorithm_vs_target_xrd_csv_with_DFT.ipynb.

Run crystal_morphing (./crystal_morphing_with_bayesian_for_xrd/crystal_morphing_main)

Crystal morphing makes intermediate structures between two input structures.

Detailed information is written in jupyter notebook, crystal_morphing.ipynb.

Also see README.md in the folder.

Run crystal_morphing with Bayesian for XRD application (./crystal_morphing_with_bayesian_for_xrd)

This process tries to find intermediate structures with higher cosine similarity of XRD pattern with respect to the target XRD.

Detailed information is written in jupyter notebook, crystal_morphing_bayesian_vs_xrd_csv.ipynb.

Utils for XRD (./utils_for_xrd & ./utils_for_xrd/cossim_vs_xrdcsv/)

Some useful scripts are included.

Detailed information is written in jupyter notebook.

Citation

If you find it useful to use this program in your research, please cite the following paper.

• Evolv&Morph

Joohwi Lee, Junpei Oba, Nobuko Ohba, and Seiji Kajita, npj Computational Materials, 9, 135 (2023). 

When accepted, the reference will be changed into an accepted journal.

• Crystal Morphing

Junpei Oba and Seiji Kajita, Physical Review Materials 6, 023801 (2022).

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